VARION: A Network Propagation Framework for Individual Patient Somatic Mutation Interpretation in Cancer Molecular Subtyping

RCoxNet: A Deep Learning Framework Integrating Random Walk with Restart, Mutation, and Clinical Data for Cancer Survival Prediction.

Accurate survival prediction in cancer remains challenging due to the sparsity of somatic mutation profiles and the failure of existing models to capture higher-order gene-gene dependencies. Network diffusion methods such as Random Walk with Restart (RWR) can propagate mutation signals across protein-protein interactio...

Graph Neural Networks for Cancer Driver Gene Prediction: From Fundamentals to Applications.

Heterogeneous graph neural networks with biological prior knowledge for interpretable drug repurposing in triple-negative breast cancer

Drug repurposing offers a cost-effective path to new therapies for triple-negative breast cancer (TNBC), a subtype with limited targeted treatment options. We present PRECISION, a framework integrating transcription factor (TF) regulatory networks, protein-protein interactions, and drug-target edges into a heterogeneou...

A Network-Guided Modular Framework for drug response prediction in acute myeloid leukemia.

Drug response prediction in acute myeloid leukemia (AML) is challenged by sample heterogeneity and high-dimensional RNA sequencing profiles. We develop NGM-AML, a modular model predicting ex vivo drug response from BeatAML2 RNA-seq and sensitivity data. After filtering, 306 Waves 1+2 samples (28055 records) serve as tr...

OncoRAG: graph-based retrieval enabling clinical phenotyping from oncology notes using local mid-size language models

OncoRAG enables accurate clinical phenotyping from multilingual oncology notes using a locally deployable mid-size model, without model weight fine-tuning or external data sharing.

Molecular therapy matching score correlates with clinical outcomes: a system for navigating cancer complexity

Historically, precision medicine implies matching one biomarker to cognate monotherapies. However, next-generation precision oncology must address cancer complexity. Indeed, advanced tumors have a median of five genomic alterations; with ~700 cancer-causing genes, there are >1 trillion patterns. We describe an algo...